Optimisation of distributed feedback laser biosensors

A new integrated optical sensor chip is proposed, based on a modified distributed- feedback (DFB) semiconductor laser. The semiconductor layers of different refractive indices that comprise a laser form the basis of a waveguide sensor, where changes in the refractive index of material at the surface are sensed via changes in the evanescent field of the lasing mode. In DFB lasers, laser oscillation occurs at the Bragg wavelength. Since this is sensitive to the effective refractive index of the optical mode, the emission wavelength is sensitive to the index of a sample on the waveguide surface. Hence, lasers are modelled as planar waveguides and the effective index of the fundamental transverse electric mode is calculated as a function of index and thickness of a thin surface layer using the beam propagation method. We find that an optimised structure has a thin upper cladding layer of ~0.15 mum, which according to this model gives detection limits on test layer index and thickness resolution of 0.1 and 1.57 nm, respectively, a figure which may be further improved using two lasers in an interferometer-type configuration

Exponential Mixing for a Stochastic PDE Driven by Degenerate Noise

We study stochastic partial differential equations of the reaction-diffusion type. We show that, even if the forcing is very degenerate (i.e. has not full rank), one has exponential convergence towards the invariant measure. The convergence takes place in the topology induced by a weighted variation norm and uses a kind of (uniform) Doeblin condition.Comment: 10 pages, 1 figur

Effect of sea ice meltwater on the alkalinity of seawater

Alkalinity values in the top few hundred meters in Baffin Bay were about 100 μeq kg—1 above those expected from deeper values when the effect of salinity is removed. This “excess” alkalinity is attributed to calcium carbonate that precipitated from brines in sea ice and was subsequently reintroduced into the water column when the ice melted. The “excess” alkalinity is then used to estimate the amount of sea ice meltwater formed in Baffin Bay

Experimental evidence for competitive N-O and O-C bond homolysis in gas-phase alkoxyamines

The extensive use of alkoxyamines in controlled radical polymerisation and polymer stabilisation is based on rapid cycling between the alkoxyamine (R1R2NO-R3) and a stable nitroxyl radical (R1R2NO•) via homolysis of the labile O-C bond. Competing homolysis of the alkoxyamine N-O bond has been predicted to occur for some substituents leading to production of aminyl and alkoxyl radicals. This intrinsic competition between the O-C and N-O bond homolysis processes has to this point been difficult to probe experimentally. Herein we examine the effect of local molecular structure on the competition between N-O and O-C bond cleavage in the gas phase by variable energy tandem mass spectrometry in a triple quadrupole mass spectrometer. A suite of cyclic alkoxyamines with remote carboxylic acid moieties (HOOC-R1R2NO-R3) were synthesised and subjected to negative ion electrospray ionisation to yield [M − H]− anions where the charge is remote from the alkoxyamine moiety. Collision-induced dissociation of these anions yield product ions resulting, almost exclusively, from homolysis of O-C and/or N-O bonds. The relative efficacy of N-O and O-C bond homolysis was examined for alkoxyamines incorporating different R3 substituents by varying the potential difference applied to the collision cell, and comparing dissociation thresholds of each product ion channel. For most R3 substituents, product ions from homolysis of the O-C bond are observed and product ions resulting from cleavage of the N-O bond are minor or absent. A limited number of examples were encountered however, where N-O homolysis is a competitive dissociation pathway because the O-C bond is stabilised by adjacent heteroatom(s) (e.g. R3 = CH2F). The dissociation threshold energies were compared for different alkoxyamine substituents (R3) and the relative ordering of these experimentally determined energies is shown to correlate with the bond dissociation free energies, calculated by ab initio methods. Understanding the structure-dependent relationship between these rival processes will assist in the design and selection of alkoxyamine motifs that selectively promote the desirable O-C homolysis pathway

Dirac spinor fields in the teleparallel gravity: comment on "Metric-affine approach to teleparallel gravity"

We show that the coupling of a Dirac spinor field with the gravitational field in the teleparallel equivalent of general relativity is consistent. For an arbitrary SO(3,1) connection there are two possibilities for the coupling of the spinor field with the gravitational field. The problems of consistency raised by Y. N. Obukhov and J. G. Pereira in the paper {\it Metric-affine approach to teleparallel gravity} [gr-qc/0212080] take place only in the framework of one particular coupling. By adopting an alternative coupling the consistency problem disappears.Comment: 8 pages, Latex file, no figures, to appear in the Phys. Rev. D as a Commen

RAFT-based polystyrene and polyacrylate melts under thermal and mechanical stress

Although controlled/living radical polymerization processes have significantly facilitated the synthesis of well-defined low polydispersity polymers with specific functionalities, a detailed and systematic knowledge of the thermal stability of the products-highly important for most industrial processes-is not available. Linear polystyrene (PS) carrying a trithiocarbonate mid-chain functionality (thus emulating the structure of the Z-group approach via reversible addition-fragmentation chain transfer (RAFT) based macromolecular architectures) with various chain lengths (20 kDa ≤ Mn,SEC ≤ 150 kDa, 1.27 ≤ Crossed D sign = Mw/Mn ≤ 1.72) and chain-end functionality were synthesized via RAFT polymerization. The thermal stability behavior of the polymers was studied at temperatures ranging from 100 to 200 C for up to 504 h (3 weeks). The thermally treated polymers were analyzed via size exclusion chromatography (SEC) to obtain the dependence of the polymer molecular weight distribution on time at a specific temperature under air or inert atmospheres. Cleavage rate coefficients of the mid-chain functional polymers in inert atmosphere were deduced as a function of temperature, resulting in activation parameters for two disparate Mn starting materials (Ea = 115 ± 4 kJ·mol-1, A = 0.85 × 109 ± 1 × 109 s-1, M n,SEC = 21 kDa and Ea = 116 ± 4 kJ·mol -1, A = 6.24 × 109 ± 1 × 109 s-1, Mn,SEC = 102 kDa). Interestingly, the degradation proceeds significantly faster with increasing chain length, an observation possibly associated with entropic effects. The degradation mechanism was explored in detail via SEC-ESI-MS for acrylate based polymers and theoretical calculations suggesting a Chugaev-type cleavage process. Processing of the RAFT polymers via small scale extrusion as well as a rheological assessment at variable temperatures allowed a correlation of the processing conditions with the thermal degradation properties of the polystyrenes and polyacrylates in the melt. © 2013 American Chemical Society.C.B.-K and M.W. gratefully acknowledge financial support from the German Research Council (DFG). M.L.C gratefully acknowledges generous allocations of supercomputing time from the Australian National Computing Facility, financial support from the Australian Research Council (ARC) Centre of Excellence for Free-radical Chemistry and Biotechnology and an ARC Future Fellowship. C.B.-K. acknowledges additional funding from the Karlsruhe Institute of Technology (KIT) in the context of the Helmholtz programs

Molecule‐Induced Radical Formation (MIRF) Reactions—A Reappraisal

Radical chain reactions are commonly initiated through the thermal or photochemical activation of purpose‐built initiators, through photochemical activation of substrates, or through well‐designed redox processes. Where radicals come from in the absence of these initiation strategies is much less obvious and are often assumed to derive from unknown impurities. In this situation, molecule‐induced radical formation (MIRF) reactions should be considered as well‐defined alternative initiation modes. In the most general definition of MIRF reactions, two closed‐shell molecules react to give a radical pair or biradical. The exact nature of this transformation depends on the σ‐ or π‐bonds involved in the MIRF process, and this Minireview specifically focuses on reactions that transform two σ‐bonds into two radicals and a closed‐shell product molecule

Luciferase-free Luciferin Electrochemiluminescence

Luciferin is one of Nature's most widespread luminophores, and enzymes that catalyze luciferin luminescence are the basis of successful commercial “glow” assays for gene expression and metabolic ATP formation. Herein we report an electrochemical method to promote firefly's luciferin luminescence in the absence of its natural biocatalyst—luciferase. We have gained experimental and computational insights on the mechanism of the enzyme-free luciferin electrochemiluminescence, demonstrated its spectral tuning from green to red by means of electrolyte engineering, proven that the colour change does not require, as still debated, a keto/enol isomerization of the light emitter, and gained evidence of the electrostatic-assisted stabilization of the charge-transfer excited state by double layer electric fields. Luciferin's electrochemiluminescence, as well as the in situ generation of fluorescent oxyluciferin, are applied towards an optical measurement of diffusion coefficients

The Fate of the Peroxyl Radical in Autoxidation: How Does Polymer Degradation Really Occur?

Bolland and Gee's basic autoxidation scheme (BAS) for lipids and rubbers has long been accepted as a general scheme for the autoxidation of all polymers. This scheme describes a chain process of initiation, propagation, and termination to describe the degradation of polymers in the presence of O2. Central to this scheme is the conjecture that propagation of damage to the next polymer chain occurs via hydrogen atom transfer with a peroxyl radical. However, this reaction is strongly thermodynamically disfavored for all but unsaturated polymers, where the product allylic radical is resonance-stabilized. Paradoxically, there is no denying that the autocatalytic degradation and oxidation of saturated polymers still occurs. Critical analysis of the literature, described herein, has begun to unravel this mystery. One possibility is that the BAS still holds for saturated polymers but only at unsaturated defect sites, where H transfer is thermodynamically favorable. Another is that peroxyl termination rather than H transfer is dominant. If this were the case, tertiary peroxyl radicals (formed at quaternary centers or quaternary branching defects) may terminate to form alkoxy radicals, which can much more readily undergo chain transfer. This process would lead to the creation of hydroxy groups on the degraded polymer. On the other hand, primary and secondary peroxyl radicals would terminate to form nonradical products and halt further degradation. As a result, under this scenario the degree of branching and substitution would have a major effect on polymer stability. Herein we survey studies of polymer degradation products and of the effect of polymer structure on stability and show that indeed peroxyl termination is competitive with peroxyl transfer and possibly dominant under some conditions. It is also feasible that oxygen may not be the only reactive atmospheric species involved in catalyzing polymer degradation. Herein we outline plausible mechanisms involving ozone, hydroperoxyl radical, and hydroxyl radical that have all been suggested in the literature and can account for the experimentally observed formation of hydroperoxides without invoking peroxyl transfer. We also show that oxygen itself has even been reported to slow the degradation of poly(methyl methacrylate)s, which might be expected if peroxyl radicals are unreactive toward hydrogen transfer. Discrepancies between the rate of oxidation and the rate of degradation have been observed for polyolefins and also support the counterintuitive notion that oxygen stabilizes these polymers against degradation. We show that together these studies support alternative mechanisms for polymer degradation. A thorough assessment of kinetic studies reported in the literature indicates that they are limited by their propensity to use models based on the BAS, disregarding the chemical differences intrinsic to each class of polymer. Thus, we propose that further work must be done to fully grasp the complex mechanism of polymer degradation under ambient conditions. Nonetheless, our analysis of the literature points to measures that can be used to enhance or prevent polymer degradation and indicates that we should focus beyond just the role of oxygen toward the specific chemical nature and environment of the polymer at hand.M.L.C. gratefully acknowledges the Australian Research Council (ARC) for a Georgina Sweet ARC Laureate Fellowship and Dr. Anya Gryn’ova, Dr. Richmond Lee, and Professor Francoise Reyniers for many stimulating discussions ̧ about autoxidation mechanisms

Organ Shape Sensing using Pneumatically Attachable Flexible Rails in Robotic-Assisted Laparoscopic Surgery

In robotic-assisted partial nephrectomy, surgeons remove a part of a kidney often due to the presence of a mass. A drop-in ultrasound probe paired to a surgical robot is deployed to execute multiple swipes over the kidney surface to localise the mass and define the margins of resection. This sub-task is challenging and must be performed by a highly skilled surgeon. Automating this sub-task may reduce cognitive load for the surgeon and improve patient outcomes. The overall goal of this work is to autonomously move the ultrasound probe on the surface of the kidney taking advantage of the use of the Pneumatically Attachable Flexible (PAF) rail system, a soft robotic device used for organ scanning and repositioning. First, we integrate a shape-sensing optical fibre into the PAF rail system to evaluate the curvature of target organs in robotic-assisted laparoscopic surgery. Then, we investigate the impact of the stiffness of the material of the PAF rail on the curvature sensing accuracy, considering that soft targets are present in the surgical field. Finally, we use shape sensing to plan the trajectory of the da Vinci surgical robot paired with a drop-in ultrasound probe and autonomously generate an Ultrasound scan of a kidney phantom.Comment: 9 pages, 11 figure